1YPN	Transferase	date	Jun 26, 1998
title	Reduced Form Hydroxymethylbilane Synthase (K59q Mutant) Crys Structure After 2 Hours In A Flow Cell Determined By Time-R Laue Diffraction
authors	J.R.Helliwell, Y.P.Nieh, J.Raftery, A.Cassetta, J.Habash, P.D.Car T.Ursby, M.Wulff, A.W.Thompson, A.C.Niemann, A.Haedener
compound		source
Molecule: Hydroxymethylbilane Synthase Chain: A Fragment: Three Domains Synonym: Porphobilinogen Deaminase Ec: 2.5.1.61 Engineered: Yes Mutation: Yes Other_details: Contains A Dipyrromethane Cofactor Linked To 242		Organism_scientific: Escherichia Coli Organism_taxid: 562 Expression_system: Escherichia Coli Expression_system_taxid: 562
symmetry	Space Group: P 21 21 2	R_factor 0.199 R_Free 0.290
crystal cell	length a length b length c angle alpha angle beta angle gamma 88.470 76.150 50.790 90.00 90.00 90.00
method	X-Ray Diffraction	resolution	2.30 Å
ligand	DPM	enzyme	Transferase E.C.2.5.1.61 BRENDA
related structures	by homologous chain: 1AH5, 2YPN
Gene Ontology	Chain Function Process Component A

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (53 Kb) [Save to disk] Biological Unit Coordinates (1ypn.pdb1.gz) 48 Kb LPC: Ligand-Protein Contacts for 1YPN CSU: Contacts of Structural Units for 1YPN Likely Quarternary Molecular Structure file(s) for 1YPN Structure Factors (86 Kb) Retrieve 1YPN in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 1YPN from S2C, [Save to disk] Re-refined 1ypn structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 1YPN in 3D

Proteopedia, because life has more than 2D. On Jmol, a nice Rasmol like molecule viewer. This is good for easiest viewing of basic structure. On FirstGlance, an excellent tool for a guided tour on the structure components, by E. Martz.

Visual 3D analysis of 1YPN

Ramachandran plot from PDBSum

Structure-derived information

Electron Density related parameters from EDS Electron Density Server, at Upsala Dipole moment, from Dipole Server at Weizmann Institute 3D motif for 1YPN, from MSDmotif at EBI Classification of representative domains in scop (Structural Classification of Proteins)     - Domain d1ypn_2, region 220-306 [Jmol] [rasmolscript] [script source]     - Domain d1ypn_1, region 3-219 [Jmol] [rasmolscript] [script source] Class (fold), Architecture (subfold), Topology, Homologous superfamily from CATH Summaries and structural analyses of PDB data files from PDBSum Identification of Protein Pockets & Cavities at CASTp

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [1ypn_A] [1ypn] SWISS-PROT database: [P06983] Domain organization of [HEM3_ECOLI] by SWISSPFAM

Other resources with information on 1YPN

Community annotation for 1YPN at PDBWiki (http://pdbwiki.org) MMDB (Entrez's Structure Database)

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